Wednesday, March 31, 2010

Why Evolutionists Say Evolution is a Fact

Evolutionists say evolution is a fact, every bit as much as gravity is a fact. That is remarkable. We see and even feel gravity everyday. Evolution, on the other hand, entails rather dramatic, one-time, events that were supposed to have occurred long ago, when no one was around to witness them. How could we be sure of such a theory? There must be some extremely powerful and compelling scientific evidence for evolution to make it a fact as gravity is a fact. That is what one would think. But, surprisingly, there is no such evidence. When evolutionists try to explain why evolution is a fact, it is a tremendous anticlimax. Consider this example from evolutionist Massimo Pigliucci:

Consider the following: if there is any obvious evidence of the fact that evolution has occurred, it ought to be the impressive and worldwide consistent fossil record. Moreover, using the geological column as a way to date events during the history of the earth predates Darwin (i.e., it was invented by creationists), and we keep discovering new intermediate fossils further documenting evolution every year.

This is astonishing.

The fossil record, of course, is not "obvious evidence" of the fact of evolution. If we want to speak of facts, the fossil record provides a wide spectrum of data which do not prove evolution. Indeed, the fossil record falsified several fundamental predictions of evolution. That is a fact. Another fact is that evolutionists make startling truth claims and then back them up with weak or even contradictory evidences. This raises the question of how evolutionists could have such certainty in light of such skimpy evidence?

The fossil column does provide important historical information, and indicates change over history. Along one lineage, we can see that at one time there were fish, but no amphibians; then there were amphibians, but no reptiles; there were reptiles, but no mammals; mammals but no primates; primates, but no hominids; hominids, but no modern humans, then modern humans.

We can directly observe evolution, including Natural Selection. It's an observed fact of nature.

"This raises the question of how evolutionists could have such certainty in light of such skimpy evidence?"

Oh! That's easy!

The single non-negotiable core commitment of evolutionism can be put into common speech as, “God didn’t do it!” Therefore, and while this non-negotiable core commitment is generally not explicitly spoken by the evolutionists, and frequently denied (as we shall no doubt see in response to my mentioning of it), all “explanations” acceptable to evolutionists must be consistent with the “It” in question being entirely accidental.

Given that the end-result “It” to be explained is the present-day biological reality, something very like Darwinism is dictated the evolutionists by their single non-negotiable core commitment. It will never matter to the True Believers that their touted “mountains of evidence” are molehills and are overshadowed by the evidence against ‘modern evolutionary theory’ (that is, Darwinism), “evolution” (equivocation) *must* be a “fact” (equivocation) -- for the only alternative to “God didn’t do it!” is “Damnitall! God did it.”

Ilion: The single non-negotiable core commitment of evolutionism can be put into common speech as, “God didn’t do it!”

Sorry, that is incorrect. The fact is that the nested hierarchy of morphology, genomes, embryonics, biogeography and fossils in time, provide strong support for diversification in stages from common ancestors. We call that process descent with modification.

We can also label those observations as the developmental unfolding of pre-existing information, which is also corroborated by evidence.

Common descent is an attempt to mislead a layperson that all branches are seamlessly connected, but when push comes to shove, you (pl) will admit it appears that organisms evolved separately on numerous occasions, thus breaking that implied seamless connection.

Moreso, the numerous instances of organisms separately evolving similar parts and functions strongly suggests common design,i.e. the unfolding of pre-existing information, not common descent.

Zachriel: "The fact is that the nested hierarchy of morphology, genomes, embryonics, biogeography and fossils in time, provide strong support..."

Err....

1. Isn't it the case that we only rarely come up with any of these nested hierarchies (of any of those sorts)?

2. Isn't it the case that when we do come up with a nested hierarchy, we hold it only very tentatively? i.e. we'd be unsurprised if the hierarchy was all wrong?

3. And isn't it the case that when we do come up with an apparently well-documented nested hierarchy, that those formed hierarchies *habitually* contradict one another despite our previous confidence (esp. Morphology vs. Genealogy; there's been a *consistently* rich history of jaw-dropping surprises)?

The fact is that the nested hierarchy of morphology, genomes, embryonics, biogeography and fossils in time, provide strong support for diversification in stages from common ancestors. We call that process descent with modification.

When a nested hierarchy is not observed, when fossils are not observed and so on it is still said that evolution is a fact.

When the illusion of a specified theory is done away with and only vague notions of "descent with modification" are left the only thing that evolutionists seems certain of with respect to their "theory" is one thing: "God didn't do it." There is only one thing that they are certain of and that is that "God did it." is false or can be safely overlooked. In my experience this is the only tenant among their contradictory theories and unfalsifiable hypotheses which is unchanging and which they are willing to specify and fight for. In Gould's The Structure of Evolutionary Theory he writes thousands of pages trying to define it, yet in the end even core tenants are remarkably vague. There is only one thing that seems to be specified for certain in this presumably "scientific" theory and that is that God didn't do it. (And not just any God, it's the God of the Jews/creationists.) Apparently the only way to falsify the core tenant of evolution is to find scientific evidence that God did do it. And that is defined as impossible. So evolution at its most specified, whatever else it may be given enough equivocation, seems to be unfalsifiable at its most specified.

Zach argued that "the theory" could be falsified in principle if centaurs and mermaids were observed. Even if that were so when all proponents of a theory can think of when it comes to illustrating its core knowledge/scientia is that it predicts that centaurs and mermaids do not exist you have to wonder about it.

Nope. Z's argument is circular (begging the question). We can directly observe different types of fossils. Evolution is but one potential explanation for the successive differences in types of fossils. It may be the correct explanation, or it may not be, but the fossils don't prove it--they merely don't exclude as a possible explanation.

Z assumes the truth of evolution, observes that fossils are consistent with that explanation, and then claims the fossils prove evolution. Classic question begging.

One can observe the same type of mistake in regard to junk DNA. Biologists assumed evolution was true, observed DNA for which they did not (yet) have an explanation function or observed function, and so "concluded" that junk DNA proved evolution (because evolution would lead to a collection of junk--a theory developed only after so-called junk was observed). Classic question begging. And what happened? Lo and behold junk DNA is finally investigated (after being ignored because of an incorrect theory (i.e., evolution) and found to have a function. The initial (question begging) argument is proved wrong.

Z's question begging regarding fossils does not "prove" evolution, just as the question begging regarding junk DNA did not prove evolution either. Z could be wrong in his theory of fossils, and so far the evidence is accumulating that he is.

Steve: We can also label those observations as the developmental unfolding of pre-existing information, which is also corroborated by evidence.

Perhaps. Let's start with what we can clearly establish. Do you agree the evidence supports divergence from common ancestors?

Steve: Common descent is an attempt to mislead a layperson that all branches are seamlessly connected, but when push comes to shove, you (pl) will admit it appears that organisms evolved separately on numerous occasions, thus breaking that implied seamless connection.

What does "seamlessly connected" mean? It would seem to be more consistent with developmental unfolding than stochastic evolutionary processes.

Steve: Moreso, the numerous instances of organisms separately evolving similar parts and functions strongly suggests common design,i.e. the unfolding of pre-existing information, not common descent.

The concept of convergence has been part of the theory of evolution since "Origin of Species." Are you familiar with Darwin's arguments in this regard?

Blake G: 1. Isn't it the case that we only rarely come up with any of these nested hierarchies (of any of those sorts)?

Actually, the nested hierarchy is very well-supported for most taxa.

Blake G: 2. Isn't it the case that when we do come up with a nested hierarchy, we hold it only very tentatively? i.e. we'd be unsurprised if the hierarchy was all wrong?

In fact, the nested hierarchy across most taxa leads to very specific empirical predictions that have been repeatedly verified.

Blake G: 3. And isn't it the case that when we do come up with an apparently well-documented nested hierarchy, that those formed hierarchies *habitually* contradict one another despite our previous confidence (esp. Morphology vs. Genealogy; there's been a *consistently* rich history of jaw-dropping surprises)?

Indeed, the nested hierarchy of morphology and genomics is highly consistent. The discrepancies occur in either rapid radiative nodes or deep in the root of the tree.

With respect to this: The fact is that the nested hierarchy of... fossils in time, provide strong support for diversification in stages from common ancestors.

An interesting contrast:...this tale exemplifies what may be called the cardinal and dominant fact of the fossil record, something that professional paleontologists learned as soon as they developed tools for an adequate stratigraphic tracing of fossils through time: the great majority of species appear with geological abruptness in the fossil record and then persist in stasis until their extinction. Anatomy may fluctuate through time, but the last remnants of a species usually look pretty much like the first representatives. ....The long term stasis, following a geologically abrupt origin, of most fossil morphospecies, has always been recognized by professional paleontologists.... This fact, as discussed on the next page, established a basis for bistratigraphic practice, the primary professional role for paleontology during most of its history.....Evolutionary theory may be a wonderful intellectual frill, but workaday paleontology, until very recently, used fossils primarily in the immensely useful activity (in mining, mapping, finding oil, etc.) of dating rocks and determining their stratigraphic sequence. These practical paleontologists dared not be wrong in setting their criteria for designation ages and environments. ....they could not let theory dictate a fancy expectation unsupported by observation. ....in fact, biostratigraphers treat species as stable entities throughout their documented ranges-because the vast majority so appear in the empirical record. (The Structure of Evolutionary Theory by Stephen J. Gould :749-751)

Yet the evidence matters little, as apparently evolution is true because God didn't do it.

Question: Isn't it the case that any nested hierarchy is also consistent with multiple hypotheses, non-exhaustively including:1) Special creation;2) Progressive creation;3) "Front-loading" evolution;4) "Interventionist" evolution;5) No evolution at all, but rather the well-known human propensity for seeong patterns where there are none.

Answer: Why, yes, it is true that nested hierarchies are logically consistent with multiple hypotheses.

Logical implication: Nested hierarchies are underdetermined with respect to Darwinism, and the Darwinist who attempts to brandish them as evidence for Darwinism is engaging in various logical fallacies, including the perennial favorites: circular reasoning and special-pleading.

mynym: When a nested hierarchy is not observed, when fossils are not observed and so on it is still said that evolution is a fact.

We don't need a continuum to reconstruct a nested hierarchy.

mynym: Zach{riel} argued that "the theory" could be falsified in principle if centaurs and mermaids were observed.

As Centaurs could be remembered creatures rather than imaginary ones, their existence is quite conceivable. Centaurs would directly contradict the expected nested hierarchy, so they would undermine current biological theory. The reason you don't consider it a reasonable example is because you intuitively recognize the nested hierarchy, even if you don't know it as such.

#John1453: We can directly observe different types of fossils. Evolution is but one potential explanation for the successive differences in types of fossils.

You're confusing the direct observation of evolution, such as in the Grants' observations of evolution in Galápagos Finches, with Common Descent, which is inferred from a variety of evidence from geology to genetics.

1. To my awareness, we've only even drawn significant trees from morphology and genomes. Surely given that alone, my first point seems to hold.

2. I don't see how this response here is relevant to my point. Can you help me out?

3. So presupposing Grice's maxim of relevance, and noting your words that the the heirarchies are "highly consistent", I take you to be implying that the mophologies and geneologies don't conflict after all.

I think this is mistaken:

In "Nature": Nature: When biologists talk of the ‘evolution wars’, they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species' morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history. … So can the disparities between molecular and morphological trees ever be resolved? Some proponents of the molecular approach claim there is no need. The solution, they say, is to throw out morphology, and accept their version of the truth. “Our method provides the final conclusion about phylogeny,” claims Okada. Shared ancestry means a genetic relationship, the molecular camp argues, so it must be better to analyse DNA and the proteins it encodes, rather than morphological characters that can end up looking similar as a result of convergent evolution in unrelated groups, rather than through common descent. But morphologists respond that convergence can also happen at the molecular level, and note there is a long history of systematists making large claims based on one new form of evidence, only to be proved wrong at a later date. [Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000)]

Likewise, another article in "Nature": Despite the comforting certainty of textbooks and 150 years of argument, the true relationships of the major groups (phyla) of animals remain contentious. In the late 1990s, a series of controversial papers used molecular evidence to propose a radical rearrangement of animal phyla. [Martin Jones & Mark Blaxter, "Evolutionary biology: Animal roots and shoots", Nature 434, 1076-1077 (28 April 2005)]

In Trends in Ecology & Evolution: [t]he wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows. [W. W. De Jong, "Molecules remodel the mammalian tree", Trends in Ecology & Evolution Tree Vol 13, No 7, pg. 270-274 (July 7, 1998)]

I.D. proponant Casey Luskin, in "Primer on the Tree of Life", provides a wealth of such citations, clearly in context, to this effect. Isn't it just irresponsible at this point to deny that there is inconsistency except in "in either rapid radiative nodes or deep in the root of the tree"?

Ilíon: Question: Isn't it the case that any nested hierarchy is also consistent with multiple hypotheses, non-exhaustively including:1) Special creation;2) Progressive creation;3) "Front-loading" evolution;4) "Interventionist" evolution;5) No evolution at all, but rather the well-known human propensity for seeong patterns where there are none.

1. Special creation is not well-defined. It can be taken to be consist with any pattern. 2. That seems to just mean creation to look like Common Descent. 3. Front-loading may be consistent with Common Descent. 4. That seems to just mean creation to look like Common Descent. 5. This one is false. We can make and verify empirical predictions based on the nested hierarchy and Common Descent.

Ilíon: Nested hierarchies are underdetermined with respect to Darwinism ...

Darwinism isn't well-defined in your context. The nested hierarchy is evidence for Common Descent, however, only some mechanisms can reasonably be said to be consistent with Common Descent.

Ilíon: 5) No evolution at all, but rather the well-known human propensity for seeong patterns where there are none.

Consider a simple case. You say you have an organism with mammary glands.

We can predict it will have a complex eukaryote cell structure with organelles, ingest other organisms for nourishment, bilateral symmetry, alimentary canal, have a bony head at one end with an array of sense organs, vertebrae protecting a nerve cord, integument, jaw, ribs, four limbs during at least at some stage of life, neck, neocortex, endothermic, internal fertilization, four-chambered heart, lungs with alveoli and a muscular diaphragm, two eyes, three ear bones in each of two ears, hair or at least hair follicles at some stage of life, sebaceous glands, most will have heterodont dentition, etc.

Centaurs would directly contradict the expected nested hierarchy, so they would undermine current biological theory. The reason you don't consider it a reasonable example is because you intuitively recognize the nested hierarchy, even if you don't know it as such.

I never disagreed with you on the general existence of a nested hierarchy. Although it would seem to matter little given that when it is not observed evolution is not considered to be falsified anyway.

Although it has been stated a priori that everyone must say that God did not do anything it is worth noting that if one was allowed to say something and if monotheism were true a nested hierarchy might be the best general structure to indicate it. Ironically the structure of a nested hierarchy is resistant naturalism, it may even be the best structure one could design in order to resist nature based views. Ancient pagans seemed to realize the possible implications of the nested hierarchy intuitively, thus they usually sought to imagine things differently as the general imagery of their idols indicate. They imagined things that way because it actually supports nature based views and or ideas about many gods and undermines monotheism. Yet those who adhere to naturalism in modern times now cite the nested hierarchy and its evidence of a common source of life as evidence for naturalism? At any rate it matters little. Only one thing seems to be certain among pagans and that is that the singular God of the Jews who creates form itself must be rejected or avoided.

Darwin: the periods during which species have undergone modification, though long as measured in years, have probably been short in comparison with the periods during which they retain the same form.

It's true that even Darwin's core tenets (memes that were tenants in his brain events) often included the exact opposite prediction. However this is not so easy to do away with by playing pretend as you typically do. Even on the page you are quoting from (in context) he did not give up on gradualism and instead argued that the fossil record was imperfect and argued that various imaginary events supported gradualism.

E.g.We shall, perhaps, best perceive the improbability of our being enabled to connect species by numerous fine, intermediate fossil links, by asking ourselves whether, for instance, geologists at some future [imaginary] period...It may be worth while to sum up the foregoing remarks on the causes of the imperfection of the geological record under an imaginary illustration.

Etc.

Although Darwin liked to wallow around in unfalsifiable hypothetical goo just like other proponents of evolutionary creation myths (It seems that it does not really matter what is observed in the fossil record, after all. Imagine that!) you haven't actually done away with Darwin's general commitment to gradualism and predictions derived from it.

The Origin, as a volume of single authorship, maintains a stronger plot line and features fewer inconsistencies than the Bible; but Darwin and the Good Lord do share the common trait of saying something about nearly everything. Wrenched from context and divorced from a crucial assessment by relative frequency, a Darwinian statement can be found to support almost any position, even the most un-Darwinian. Since Darwin prevails as the patron saint of our profession, and since everyone wants such a preeminent authority on his side, a lamentable tradition has arisen for appropriating single Darwinian statements as defenses for particular views that either bear no relation to Darwin's own concerns, or that even confute the general tenor of his work. ....I raise this point here because abuse of selective quotation has been particularly notable in discussions of Darwin's views on gradualism. Of course Darwin acknowledged great variation in rates of change, and even episodes of rapidity that might be labeled catastrophic... But these occasional statements do not make Darwin the godfather of punctuated equilibrium, or a cryptic supporter of saltation... Gradualism may represent the most central conviction residing both within and behind all Darwin's thought. .... Gradualism sets the explanatory framework for his first substantive book on coral reefs (1842) and for his last on the formation of topography and topsoil by earthworms (1881)-two works largely devoid of reference to natural selection. Gradualism had been equated with rationality itself by Darwin's chief guru, Charles Lyell. ....I will not play "dueling quotations" with "citation grazers," though a full tabulation of relative frequencies could easily bury their claims under a mountain of statements.(The Structure of Evolutionary Theory by Stephen J. Gould :148-149) (Emphasis added)

We would prefer a direct answer. Do you agree the evidence supports divergence from common ancestors?

Blake G: In Trends in Ecology & Evolution: [t]he wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows. [W. W. De Jong, "Molecules remodel the mammalian tree", Trends in Ecology & Evolution Tree Vol 13, No 7, pg. 270-274 (July 7, 1998)]

The paper doesn't say what you think it does. The evolutionary relationships of closely related organisms can be difficult to resolve, especially with the limited data available in 1998. If you read the paper, it is clear that there is a tree, but with many unresolved elements. The authors say that additional data will help resolve the relationships.

As expected, more data confirms the basic tree-like topology and provides additional detail on the transitions.

Prasad et al., Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets, Molecular Biology and Evolution 2008:

Our studies highlight the difficulties in resolving some very short mammalian branches (e.g., interordinal relationships within Laurasiatheria), even with large amounts of data. Our work further illustrates the value of large genomic sequence data sets for improving the resolution of phylogenetic trees, in this case, to clarify some of the remaining ambiguities within the mammalian tree. Sequences from an increasing number of mammalian taxa should help to resolve the remaining ambiguities associated with the short branches within and between the placental orders.

If you weren't so busy trying to suckle at the teat of Mother Nature you would know that the nested hierarchy and common structures and patterns to life do not necessarily support your evolutionary creation myths.

Now it seems that you've implied that Darwin did not predict much of anything about what should be observed in the fossil record.

Perhaps you agree with these supposed specifications:Deduction 1: If the hypothesis of evolution is true, the species that lived in the remote past must be different from the species alive today.....Deduction 2: If the hypothesis of evolution is true, the older the sedimentary data, the less the chance of finding fossils of contemporary species.....Deduction 3: If the hypothesis of evolution is true, then we would expect to find only the simplest organisms in the very oldest fossiliferous strata and the more complex ones only in the more recent strata.....Deduction 4: If the hypothesis of evolution is true, it must be possible to demonstrate the slow change of one species into another. ....Deduction 5: If the hypothesis of evolution, which assumes that all of today's species are the descendants of a few original forms, is true, there should have been connecting forms between the major groups (phyla, classes, orders).(Science as a Way of Knowing: The Foundations of Modern Biology by John A. Moore :148-154)

mynym: Ironically the structure of a nested hierarchy is resistant naturalism, it may even be the best structure one could design in order to resist nature based views.

Actually, the nested hierarchy is a direct consequence of divergence along uncrossed lines.

mynym: It's true that even Darwin's core tenets (memes that were tenants in his brain events) often included the exact opposite prediction.

That is incorrect. The statement that long as measured in years is short in geological terms is very much part of Darwin's thought.

mynym: Although Darwin liked to wallow around in unfalsifiable hypothetical goo just like other proponents of evolutionary creation myths (It seems that it does not really matter what is observed in the fossil record, after all.

Ironically, Darwin was considered a biologist and observer of the first rank, even before Origin of Species. And still is. Consider that his theory has spawned more than a century of inquiry in many different fields of study. His treatise on earthworms was an instant classic.

mynym: Oh well, at least it predicts every organism that has ever been observed.

mynym: the nested hierarchy and common structures and patterns to life do not necessarily support your evolutionary creation myths.

The question was raised as to whether there was a real pattern, or only one imposed by observational bias. It's a real pattern, because it entails verifiable empirical predictions.

mynym: Now it seems that you've implied that Darwin did not predict much of anything about what should be observed in the fossil record.

He predicted that every newly discovered fossil would fit the nested hierarchy predicted from Common Descent.

mynym: Deduction 1: If the hypothesis of evolution is true, the species that lived in the remote past must be different from the species alive today....Deduction 2: If the hypothesis of evolution is true, the older the sedimentary data, the less the chance of finding fossils of contemporary species.

That is incorrect. Organisms well adapted to their niche may change very little. Darwin coined the term "living fossils."

mynym: Deduction 3: If the hypothesis of evolution is true, then we would expect to find only the simplest organisms in the very oldest fossiliferous strata and the more complex ones only in the more recent strata.

Evolution doesn't necessarily proceed from simple to complex.

mynym: Deduction 4: If the hypothesis of evolution is true, it must be possible to demonstrate the slow change of one species into another.

Speciation can be fast or slow. Complex adaptation has to be in incremental steps.

mynym: Deduction 5: If the hypothesis of evolution, which assumes that all of today's species are the descendants of a few original forms, is true, there should have been connecting forms between the major groups (phyla, classes, orders).

Yes. You had said you accepted that the evidence supports divergence from common ancestors.

Zachriel: "The paper doesn't say what you think it does. ... If you read the paper, it is clear that there is a tree, but with many unresolved elements."

It's interesting that you only responded to one of my citations. No matter. The paper discusses "[t]he wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush"I'm curious as to why you would think I was citing the paper as evidence that there was no tree, when the context of our discussion indicates that rather I'm arguing for their being, in fact, multiple trees (in this case, morphological vs. geneological)... and that they are "unresolved" (or "competing", in the papers words). What exactly is my error, then?

You then curiously cited a different paper that suggested "Use of Large Comparative Sequence Data Sets" could help clear things up. But have they been cleared up? Certainly not to my knowledge. That paper is from 2008, but as NewScientist emphasized in 2009, and I quote:

"It's part of a revolutionary change in biology," says Dupré "Our standard model of evolution is under enormous pressure. We're clearly going to see evolution as much more about mergers and collaboration than change within isolated lineages." Rose goes even further. "The tree of life is being politely buried, we all know that," he says. "What's less accepted is that our whole fundamental view of biology needs to change."[...] "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?" [Graham Lewton, (21 Jan 2009) # 2692.]

The paper emphasizes that these conflicts are not simply at life's roots, contra your first response; they pervade throughout. BTW, there's a whole slew of citations in that article as well which make my point (in addition to all those given in the "Primer on the Tree of Life" article I referenced you to).

You didn't respond to the other citations I gave in my post above, so I don't want to flood you, but here's a few more:

Proceedings of the National Acadamy of Sciences: "[p]hylogenetic [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves." [Carl Woese, PNAS June 9, 1998 vol. 95 no. 12 6854-6859]

Journal of Molecular Evolution: That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent. [Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, "Novel Phylogeny of Whales Supported by Total Molecular Evidence," Journal of Molecular Evolution 44 (Supplement 1, 1997): S117-S120]

Annual Review of Ecology and Systematics: As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology [Patterson et al., "Congruence between Molecular and Morphological Phylogenies", Annual Review of Ecology and Systematics, vol 24, pg. 179 (1993)]

This is my take on the 5 deductions from The Foundations of Modern Biology.

I concur in the use of the word “hypothesis”, since evolution has not yet achieved the status of “theory”.

Deductions 1, 2, and 3 are “retrodictions” that are really not very helpful in demarcating between evolution and other hypotheses.

Deduction 4 does have the potential of providing a demarcation criterion for distinguishing between evolution and other hypotheses. John A. Moore is emphatic: It must be possible to demonstrate the slow change of one species into another. The fact that Moore considers this a possibility means that the demonstration of slow change hasn’t yet occurred (at least as of the date of publication of his book.)

But, is the speed of the change the real issue? And, are we not only concerned with the change of one species into another, but also with the change of one body plan into another?

Deduction 5 refutes itself. When Moore says there should have been connecting forms between the major groups, he has already admitted that the connecting forms are missing. Therefore, by his own admission, the hypothesis of evolution is falsified.

It is also interesting to note that he assumes common descent rather than pose it as a testable hypothesis.

Note: I wrote the above off-line before I saw Zachriel’s response. Here I my responses to his comments.

I agree with a couple of things that Zachriel said, with qualifications.

Re: Deduction 2

Zachriel says deduction 2 is incorrect.

I say it is correct, but problematic. The proposition states that there is less chance of finding a fossil resembling an extant species in the older sedimentary data. My quibble is with the use of the phrase “less chance.” Moore does not rule out that we won’t find similar fossils, only that we would find very few of them. The problem is that seems to set some kind of vague boundary condition on the number of fossils we would expect to find. A larger number of similar fossils would tend to refute the hypothesis; a lesser number would tend not to refute it. What is that number?

Re: Deduction 4

I also questioned the speed of evolutionary change as a demarcation criterion. I find it interesting that Zachriel did not comment on the requirement that science must be able to demonstrate how the change takes place before we can conclude whether evolution is true.

Blake G: It's interesting that you only responded to one of my citations.

Just picked one that look interesting. (They were all presumably taken from secondary sources.)

Blake G: I'm curious as to why you would think I was citing the paper as evidence that there was no tree, when the context of our discussion indicates that rather I'm arguing for their being, in fact, multiple trees (in this case, morphological vs. geneological)... and that they are "unresolved" (or "competing", in the papers words). What exactly is my error, then?

This is the original exchange.

Zachriel: Indeed, the nested hierarchy of morphology and genomics is highly consistent. The discrepancies occur in either rapid radiative nodes or deep in the root of the tree.

Blake G: I take you to be implying that the mophologies and geneologies don't conflict after all."

Which, of course, was contrary to our statement, while our statement was consistent with the results of the paper Molecules remodel the mammalian tree, which strongly supports phylogeny but points to problems resolving particular branchings.

You're trying to resolve a distant tree, an oak. The overall structure of the tree can be discerned, but not every branching. Different observers think they can resolve one branching or another, but they disagree. Someone brings out a telescope, and suddenly, many of the blurry nodes can be resolved into the familiar tree-like pattern. But some are still unclear. Different observers make somewhat different conclusions. But none of them doubt the overall structure of the tree. They're only quibbling over the particulars. And the additional data supports that with regards to mammalian ordinal phylogeny. Returning to your argument.

Blake G: arguing for their being, in fact, multiple trees

For the vast majority of taxa the morphological and genetic data form the same phylogeny. But resolution remains a problem in cases.

Blake G (quoting): "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely,"

From the same article.

Nobody is arguing - yet - that the tree concept has outlived its usefulness in animals and plants.

Blake G (quoting): The paper emphasizes that these conflicts are not simply at life's roots, contra your first response; they pervade throughout.

Let's dispense with the Molecules remodel the mammalian tree paper first. The problem the researchers had resolving mammalian phylogeny had mostly to do with resolution, much of which has improved considerably over the last decade. So if that were your point, then it was the wrong paper to point to.

There is no doubt that horizontal mechanisms are essential to understanding the early evolution of life. But for many taxa of interest (most of multicellular life), the phylogenetic tree is alive and well, as we know from all the studies resolving the branchings of those taxa. Even then, there are many known cases of horizontal mechanisms, such as endogenous retroviruses, hybridization, and so on. There's even a very interesting anomaly at the *root* of placentals. Nevertheless, the nested hierarchy is strongly supported across most of those taxa. It's not a perfect tree. Sometimes branches do cross. That happens in real trees, too.

There has been a bit of overstatement that then leads to taking things out of context. And you really need to look at the original papers to see what the authors are talking about. When you pull them off of ID apologetics sites, they tend to be garbled.

It's interesting that you would point to that example. The molecular evidence caused paleontologists to reconsider their view of whale evolution, which was based on a very limited number of fossils. It resulted in expeditions that confirmed the molecular evidence. So you have molecules in living whales predicting the content of rocks found in the wastelands of South Asia. So yes, phylogeny is powerful enough to make verifiable empirical predictions.

Actually, the nested hierarchy is a direct consequence of divergence along uncrossed lines.

Actually you're just imagining things about the past. Occasionally even biologists have condemned this pattern of passing off your imagination as the equivalent of facts or empirical evidence.

That is incorrect.

Not at all, it is correct to say that Darwin predicted all possible observations with respect to the fossil record.

The statement that long as measured in years is short in geological terms is very much part of Darwin's thought.

Exactly, which combined with his arguments about imaginary events "predict" that the fossil record will contain intermediaries and also predicts that it will not. Evidence of this sort seems overwhelming to you, doesn't it?

Ironically, Darwin was considered a biologist and observer of the first rank, even before Origin of Species. And still is.

Of course, although a giant among other midgets may come up short. Other eugenicists were also considered biologists of the first rank, yet how did all these geniuses go so far wrong in that area?

Consider that his theory has spawned more than a century of inquiry in many different fields of study.

No one really knows but it is likely that it has stifled just as much as it has inspired. I'm sure it has inspired some. It is also possible to use excrement as fertilizer.

His treatise on earthworms was an instant classic.

Indeed, yet if you take his idiotic way of thinking about biology to its logical conclusion then one may as well study natural selection operating on worms rather than his words.

New organisms, extinct and extant, are continually being discovered.

Of course, it seems that every single organism that has ever existed or will exist is perfectly predicted and makes perfect sense in light of evolution, whatever it is.

Why do evolutionists insist on using the tree of life as proof of Darwinian evolution? It can equally serve as evidence for design. Designs certainly evolve over time and can be classified or organized as a tree. For example, one can use tree classification to show the evolution of computer designs starting from Jacquard's automated loom and Pascal's calculator and moving through Babbage's analytical engine, the typewriter, the vacuum tube machines of the fifties, televisions, the solid state computers of the sixties, the integrated circuit computers of the 80s to the multicore machines of today.

Using the tree of life and its discovery in the fossil record as proof of Darwinian evolution is one of those weak arguments of the evolutionist camp. Heck, even Genesis (the ultimate creation book) mentions the Tree of Life, for crying out loud.

He predicted that every newly discovered fossil would fit the nested hierarchy predicted from Common Descent.

This claim fits with all hypotheses of origins which trace back to a common source.

mynym: Deduction 2: If the hypothesis of evolution is true, the older the sedimentary data, the less the chance of finding fossils of contemporary species.

That is incorrect. Organisms well adapted to their niche may change very little. Darwin coined the term "living fossils."

I did not specify the "theory" of evolution that way, Moore did. Of course evolution predicts finding less contemporary fossils as well as finding many. Given that it predicts everything and nothing makes sense without it that's not surprising.

Evolution doesn't necessarily proceed from simple to complex.

Of course, it never necessarily predicts or does one specific thing or another. In fact, it's not even clear if it generally predicts one thing or another. At any rate, at least it does not predict centaurs. Is there any other type of organism it does not predict?

Speciation can be fast or slow. Complex adaptation has to be in incremental steps.

I don't know Zach, you seem to be implying a specification of some sort or another there. So must these imaginary incremental steps be fast or slow? Or have they already been observed?

Yes. You had said you accepted that the evidence supports divergence from common ancestors.

Of course, but how common are the ancestors and where, when and how did they diverge? Your claims are as vague as the ID claims that they're in a dialectic with. They avoid specifying the nature of the designer, you do not specify the nature of evolution. This is all well and good but let's not pretend that it's the epistemic equivalent of rigorously specified scientific theories. (And if what you and other Darwinists are doing is science then what proponents of ID are doing is equally science.)

I really appreciate your responding, and doing so in a civil manner (it's hard to find someone who will do that often). Unfortunately, I feel that my points are not being addressed.

Step 1. You said, "The fact is that the nested hierarchy of morphology, genomes, embryonics, biogeography and fossils in time, provide strong support..."

Step 2. I challenged the notion of such a thing with three points. You responded to the third point, where I wrote: "And isn't it the case that when we do come up with an apparently well-documented nested hierarchy, that those formed hierarchies *habitually* contradict one another despite our previous confidence (esp. Morphology vs. Genealogy; there's been a *consistently* rich history of jaw-dropping surprises)?"

Step 3. You said no. Insisting that the discrepancies that occur are simply those "in either rapid radiative nodes or deep in the root of the tree."

Step 4. I challenged this by citing *many* sources which suggest the opposite.

Step 5. You only targeted one of those sources, basically saying "you misread this, he's not saying there is no tree"

Step 6. I said "I never claimed there was no tree.. I claimed the opposite: There are multiple competing trees".

But First: It's not mere "particular branchings", but *enough* branchings that the authors felt warranted in saying "[t]he wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an UNRESOLVED BUSH (My emphasis)".)

Second. That's just irrelevant. How is your claim here in Step 7 pertinent at all to our discussion? I could grant it and my point would still remain! I just don't feel like i'm being properly engaged here : ( Perhaps you think I'm claiming that these particular authors here *believe* there are multiple conflicting trees *in reality*, as opposed to one tree that is just blurry from a distance (as you say). If you think this, then let stop you there. You've lost sight of the discussion: One again, cf. step #1. We're discussing your claim that we have these beautiful nested heirarchies. You wrote: "The fact is that the nested hierarchy of morphology, genomes, embryonics, biogeography and fossils in time, provide strong support for diversification in stages from common ancestors."If we have a sloppy resolution, such that it looks even remotely like a *bush* (anything other than a nice nested tree), then we're hardly warranted in saying stuff like that.

In addition to having a sloppy resolution, the veracity of the nested hierarchy is itself under fire. In addition to the many articles cited, I just found this as well:

"It takes the form of nested hierarchies that are presumed to be the consequences of descent with modification and speciation. [...] In the last several years, the increased availability of molecular data from many organisms, especially microbes, has thrown these traditional assumptions into disarray, [...] The blurring of species boundaries by hybridization is well known in plants, fungi and, increasingly, in animals. Genetic flux across all domains of life (such as that facilitated by the cross-taxa dispersal of viruses), plus other activities that produce conflicting phylogenetic signals, demand more complex ways of representing evolutionary processes than can be captured by a single tree of bifurcating branches. [...] Molecular phylogeneticists who have directly confronted the issue of the uniqueness of the ToL [Tree of Life] have found themselves forced to re-evaluate the tree’s epistemological status and downgrade it from a biological fact to a hypothesis that remains unconfirmed in relation to most life and evolutionary history. [http://centres.exeter.ac.uk/egenis/research/QuestioningtheTreeofLife.htm]

You write: "The problem the researchers had resolving mammalian phylogeny had mostly to do with resolution, much of which has improved considerably over the last decade."But "improved considerably" is awfully vague. They are *still* talking about a bush-like appearance, Zach. I both directly cited and referenced you to works which cited pieces that give this same assessment within the couple years (and certainly within the past decade). Look at this 2006 article by famously staunch Darwin apologist Sean B. Carroll and Antonis Rokas "Bushes in the Tree of Life", where they, far from thinking major resolution challenges have retreated, write: "we examine how the combination of the spacing of cladogenetic events and the high frequency of independently evolved characters (homoplasy) limit the resolution of ancient divergences.". Carrol acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, REGARDLESS [my emphasis] of the quantity of conventional data available.” The paper even contends that “the recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040352]

Perhaps most peculiar of all is your talking about whale evolution.

Step 1. I quote the Journal of Molecular Evolution, which says: That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent. [Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, "Novel Phylogeny of Whales Supported by Total Molecular Evidence," Journal of Molecular Evolution 44 (Supplement 1, 1997): S117-S120]

Step 2. You start talking about Whale evolution!

What What? The point of the quote is that here again we have sources conceding the point: "That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists" because of the incongruences.

For one to get this badly of topic doesn't bode well for any potential conversation we could continue with, I'm afraid. And I say that with regret, because I genuinely appreciate your cordial demeanor. If we were in voice chat, it'd be worth it (I could just interrupt you and say "So?" and keep us on track). It's too hard in blog comments, though.

Zachriel: Actually, the nested hierarchy is a direct consequence of divergence along uncrossed lines.

mynym: Actually you're just imagining things about the past.

It's a mathematical statement. When we have descent with variation along uncrossed lines, the patterns of variation will form a nested hierarchy (short of saturation).

mynym: Deduction 1: If the hypothesis of evolution is true, the species that lived in the remote past must be different from the species alive today.

Zachriel: That is incorrect. Organisms well adapted to their niche may change very little. Darwin coined the term "living fossils."

mynym: Not at all, it is correct to say that Darwin predicted all possible observations with respect to the fossil record.

No, Darwin predicted a nested hierarchy.

mynym: Exactly, which combined with his arguments about imaginary events "predict" that the fossil record will contain intermediaries and also predicts that it will not.

Fossilization may or may not occur. But if fossils are found, they will fit the nested hierarchy. We know enough of fossilization and evolutionary history, though, to make educated guesses about possible finds.

Zachriel: Ironically, Darwin was considered a biologist and observer of the first rank, even before Origin of Species. And still is.

mynym: Of course, although a giant among other midgets may come up short.

His peers include generations of biologists. You seem to be devolving into name-calling.

Zachriel: {Darwin} predicted that every newly discovered fossil would fit the nested hierarchy predicted from Common Descent.

mynym: This claim fits with all hypotheses of origins which trace back to a common source.

That's right. By itself descent with modification does not tell us what the mechanism might be, though not all mechanisms will be consistent with descent with modification.

Common Descent is one of the most profound facts in biology. It explains why we can look at a lower jaw comprised of a single bone with heterodont dentition, and know the organism cared for its young. As Common Descent is very well-established for most taxa, that puts limits on plausible mechanisms.

mynym: So must these imaginary incremental steps be fast or slow? Or have they already been observed?

Darwin looked that the history of life and inferred evolution. In other words, he had evidence of evolutionary history, but couldn't directly observe the process of evolution. Today, we can! We can measure its rate. That rate is much, much faster than required to explain what we see in evolutionary history.

Evolutionary rates, as Darwin already knew, varied substantially. But we now know that evolution can be quite rapid (though long as measured in years), especially during adaptive radiations.

mynym: Of course, but how common are the ancestors and where, when and how did they diverge? Your claims are as vague as the ID claims that they're in a dialectic with.

There's an entire field devoted to that question. The answers are available, if you are interested.

Louis Savain states: "Why do evolutionists insist on using the tree of life as proof of Darwinian evolution? It can equally serve as evidence for design. Designs certainly evolve over time and can be classified or organized as a tree. For example, one can use tree classification to show the evolution of computer designs starting from Jacquard's automated loom and Pascal's calculator and moving through Babbage's analytical engine, the typewriter, the vacuum tube machines of the fifties, televisions, the solid state computers of the sixties, the integrated circuit computers of the 80s to the multicore machines of today.

I assume from your latter reference to Genesis (not quoted above), that you attend this argument as a creationist who believes in an all-knowing, all-powerful god. While your analogy is useful, it indicates that such a god is unlikely to be responsible for the nested biological hierarchy.

The progression in human computer technology you discuss has a known cause: human technological limitations. As we invent and implement new technologies, computers have improved. This is the cause of the nesting - our limitations. If we had perfect knowledge we would simply create some sort of optimal computer that does not currently exist; we would not start with the abacus, nor build rooms full of valves. In short we would not have experienced said progression and no nesting would exist.

We further know that analogous things happen in the 'tree of life'. If such is the result of a designer, then the pattern of increasing complexity over the history of life at least suggests similar limitations in that designer.

To be sure, we can never know the mind of god, if such a mind exists. Hence, no argument in this line can rule out the possibility that god did it. However, we are left with no plausible reason why supernatural design would result in this pattern, excepting the vague notion that god is mysterious.

On the other hand, we are left with a highly plausible explanation for this pattern via natural processes. The process is not guided by a designer with a plan in mind and so progress from simplicity to complexity might occur via mutation and differential survival. This is why 'evolutionists' see the nested hierarchy of life as evidence in favour of naturalistic evolution, rather than design.

I underamd that he fossil record shows any change that has happened since the Devonian has occured mostly to vertebrates. Invertebrates, which compromise th overwhelming majority of species have not evolved much at all. And all the basic body types showed up in the Cambrian. Most of the changes between the Cambrian and the Devonian were just tinkering with the basic template. So the overall pattern of the fossil record is that not much evolution has happened.

laugh out loud: And all the basic body types showed up in the Cambrian. Most of the changes between the Cambrian and the Devonian were just tinkering with the basic template. So the overall pattern of the fossil record is that not much evolution has happened.

After all, humans are 'just' elaborated Deuterostomes. Tubes with appendages to stuff food into one end. Microevolution.

laugh out loud: But the overall pattern for the since the Devonian has been not much evolution.

Since the Devonian?

That's right, as long as you think a fishopod to humans is "not much evolution." Or a world with dinosaurs, birds, salmon, whales, lions and tigers and bears, oak forests, grasses, or flowers of all types is "not much" different from one without.

It's a mathematical statement. When we have descent with variation along uncrossed lines, the patterns of variation will form a nested hierarchy (short of saturation).

It seems that you really want to play pretend that you are not playing pretend. Yet you are still assuming and imagining things about origins. Other proponents have admitted that observing patterns of this sort are not necessarily evidence of common ancestry:...a cladogram is simply a branching diagram of relationships between three or more taxa. It does not specify whether one taxon is ancestral to another; it only shows the topology of their relationships as established by shared derived characters. In its simplicity and lack of additional assumptions, it is beautifully testable and falsifiable...The nodes are simply branching points supported by shared derived characters, which presumably represent the most recent hypothetical common ancestry of the taxa that branch from that node. ... Many scientists, however, would like to say more than just "taxon A is more closely related to taxon B than it is to taxon C." Instead, they would draw relationshipos with one taxon being suggested as ancestral to another.(Evolution: What the Fossils Say and Why It Matters by Donald Prothero :133-134)

Common Descent is one of the most profound facts in biology.

You seem to be confusing your assumptions with facts. You just agreed that observed patterns are consistent with any hypothesis of common origins, yet now you are stating that common ancestry is a fact?

It explains why we can look at a lower jaw comprised of a single bone with heterodont dentition, and know the organism cared for its young.

We know such things because of observed patterns in nature which have a common source. We do not know such things as a result of imagining things about hypothetical ancestors. That is merely a gloss or a creation myth added to the science. If you want to argue that your assumptions or creation narratives are reasonable that is one thing but equating assumptions with "facts" or observations is the work of charlatans.

Even a propagandist for evolutionary creation myths like Prothero cites a refutation of assuming evidence of ancestry approvingly:That a known fossil or recent species, or higher taxonomic group, however primitive it might appear, is an actual ancestor of some other species or group, is an assumption scientifically unjustifiable, for science never can simply assume that which it has the responsibility to demonstrate... --Gary Nelson (Prothero :133)

Yet he goes on to argue that imagining common ancestry is the only reason to recognize the pattern in the first place:The debate was all about whether we could tell whether a particular fossil could be recognized as an ancestor and how to do phylogeny, but even the most hard-core cladists do not doubt that [the imaginary] ancestors existed!(:135)

This is false. I can imagine, and not without reason, that the pattern can be recognized without linking its recognition to Common Descent. (I like the caps and the supposed specification of a scientific theory. Is there a singular theory of common descent or a few?) After all, Linnaeus generally recognized it. And even people who like imagining things about ancestry and creation myths recognize that the pattern is consistent with a common source but is not evidence of common ancestry. Some have even said that it is an assumption that is "scientifically unjustifiable" based on the nested hierarchy alone. It seems that if the tree of life is not rooted in imaginary evidence then it tends to die.

That last quote should be:The debate was all about whether we could tell whether a particular fossil could be recognized as an ancestor and how to do phylogeny, but even the most hard-core cladists do not doubt that [the imaginary] ancestors existed! None of the debate is about whether life has evolved. After all, what would be the point of doing a cladogram, which is [imagined to be] a phylogeny, if you didn't accept the fact of evolution?

It's curious, what other facts must be imagined to be instead of observed to be?

Darwin looked that the history of life and inferred evolution. In other words, he had evidence of evolutionary history, but couldn't directly observe the process of evolution. Today, we can! We can measure its rate.

Of course, it seems that is as it must be given that all known organisms and rates of change are predicted by evolution.

Although Moore in Science as a Way of Knowing: The Foundations of Modern Biology spent a good deal of time arguing that there is a specified theory of evolution which predicts what sort of fossil evidence should be found it seems that it matters little. As Dawkins has said:If every fossil were magicked away, the comparative study of modern organisms, of how their patterns of resemblances, especially of their genetic sequences, are distributed among species, and of how species are distributed among continents on islands, would still demonstrate, beyond all sane doubt, that our history is evolutionary, and that all living creatures are cousins. .... The fossil record could be one big gap, and the evidence for evolution would still be overwhelmingly strong.(The Ancestor's Tale by Richard Dawkins :13)

That rate is much, much faster than required to explain what we see in evolutionary history.

Apparently you need not explain anything about evolutionary history because every single organism that exists has been predicted by the theory. I wonder if each one is predicted to the same extent or if it's that predicting each and every gene, organism and species is overwhelming when taken altogether?

Your arguments that the nested hierarchy (tree of life) only fits a Darwinian evolution are unconvincing.

And abimer, I am not a creationist in the usual sense of the word. Although I am a Christian, I believe that most of the early part of the book of Genesis is metaphorical. I believe that the six days of creation, the garden of Eden, the tree of life and the tree of knowledge are all metaphors. I believe that the two trees symbolize special knowledge about life (genetics) and intelligence (brain organization) that the creator did not want humans to play with. And yes, I also believe that the brain uses a tree-like hierarchy to store and organize knowledge as it learns.

mynym: Ironically the structure of a nested hierarchy is resistant naturalism, it may even be the best structure one could design in order to resist nature based views.

Zachriel: Actually, the nested hierarchy is a direct consequence of divergence along uncrossed lines.

mynym: Actually you're just imagining things about the past.

Zachriel: It's a mathematical statement. When we have descent with variation along uncrossed lines, the patterns of variation will form a nested hierarchy (short of saturation).

mynym: It seems that you really want to play pretend that you are not playing pretend. Yet you are still assuming and imagining things about origins.

Except you didn't actually argue with the statement. It's very difficult to hold a conversation when you let the topic slip. That's why it is so often necessary to repeat entire threads of that discussion. Here is your statement again.

mynym: Ironically the structure of a nested hierarchy is resistant naturalism, it may even be the best structure one could design in order to resist nature based views.

It is a mathematical truism that divergence along uncrossed lines leads to a nested hierarchy (short of saturation). An elaborated nested hierarchy pattern doesn't require artifice: It is the inevitable consequence of the very natural processes of divergence and reproductive isolation.

Zachriel: Common Descent is one of the most profound facts in biology.

mynym: You seem to be confusing your assumptions with facts.

Common Descent is very well-supported. You have already stated "Of course the evidence supports divergence from common ancestors."

mynym: You just agreed that observed patterns are consistent with any hypothesis of common origins, yet now you are stating that common ancestry is a fact?

Use exact quotes, please. For instance, the so-called hypothesis of Front Loading depends on Common Descent.

Zachriel: It explains why we can look at a lower jaw comprised of a single bone with heterodont dentition, and know the organism cared for its young.

mynym: We know such things because of observed patterns in nature which have a common source.

Sorry, but just saying "common source" is scientifically meaningless. Common Descent explains and predicts new observations.

mynym: We do not know such things as a result of imagining things about hypothetical ancestors.

For instance, we can often predict the characteristics of intermediate organisms and then find their fossils in the appropriate strata.

mynym: Even a propagandist for evolutionary creation myths like Prothero ...

That's what is known as a quote-mine. We could dig up a family cemetary and not be able to determine the exact relationships, even if we might be able to determine that they are all cousins of one order or another. When we find a fossil, we can never be sure they are on the direct line of descent. That's why cladograms don't typically show organisms at the nodes.

mynym: I can imagine, and not without reason, that the pattern can be recognized without linking its recognition to Common Descent.

The nested hierarchy is an inevitable consequence of observed processes in nature, such as descent with modification and reproductive isolation. Just like planetary orbits are the inevitable consequence of gravitational forces and momentum. The fossil record supports descent with modification.

mynym: Some have even said that it is an assumption that is "scientifically unjustifiable" based on the nested hierarchy alone.

Well, not from your quote-mine. The statement concerned whether you could determine if a particular fossil was in the direct line of descent (rarely possible) or just a close cousin of the common ancesetor.

I unerstand that Tiktaalik is no longer considered an ancestor of tetrapods. It is, at best, a side branch that died out. The same thing is happening wth archaeopteryx and Ida, the lemur/monkey. And most of the intermediates for the majority of taxa are still missing. So I'm not sure that the overall pattern supports this view.

Louis Savain: Your arguments that the nested hierarchy (tree of life) only fits a Darwinian evolution are unconvincing.

That's not what we said in response to your last comment.

Louis Savain: Why do evolutionists insist on using the tree of life as proof of Darwinian evolution?

Zachriel: The nested hierarchy is strong evidence of Common Descent.

The nested hierarchy of genomes, morphology, embryonics, biogeography, fossils in time, is strong evidence of Common Descent. Common Descent is a profoundly important fact about biology. It means humans descended from ancestral hominids that descended from ancestral primates. There are many biological theories that might conceivably be consistent with Common Descent.

Having established Common Descent, we can discuss those various theories. But there is no escaping the fact that life has descended from common ancestors.

laugh out loud: I unerstand that Tiktaalik is no longer considered an ancestor of tetrapods.

It's an intermediate form very close to the common ancestor.

laugh out loud: And evolution happens too slow to be observed, but it happens too fast to be caught in the fossil record, hence punctuated equilibrium. So it is sort of a Goldilocks thing, it is just right.

We can observe evolution, even measure its rate. Fossilization is a very happenstance process. There are billions of fossils, but finding one close to an important transition can be problematic, as a lot of adaptive radiation occurs rapidly in small, isolated populations.

Laugh Ot Loud: "And evolution happens too slow to be observed, but it happens too fast to be caught in the fossil record, hence punctuated equilibrium. So it is sort of a Goldilocks thing, it is just right."

But tyhe real ancestor is still missing. And teh modern lungfish is close to the transitional condition, also.

Adn have we actually observed hwo long it takes for one species to turn into another? That's waht evolution means. And if there are billions of fossils, I for one, would expect to find a fw more actual transitions, and even more close to important transitions. But that's just me.

Laugh: "And have we actually observed how long it takes for one species to turn into another? That's what evolution means."

Actually, your statements are wrong on at least two points:

1) Mere speciation is a distraction from “what evolution means,” and the distraction appears to be intentional of the part of the evolutionists.

The problem for evolutionists (and it’s insurmountable for Darwinists -- hence their continuous hostility and vileness upon being questioned) is not mere speciation, but rather novel biological structures and organs, novel biological information.

2) The actual meaning of the word ‘evolution’ is nothing at all like (Darwinistic) evolutionists use it … it’s for this reason that St. Chuckie avoided the word, using instead the awkward locution, “descent with modification,” until Huxley had made it safe, so to speak, to apply the term to Darwin’s ideology.

The word ‘evolution’ is inherently teleological in meaning. It was coined in embryology to denote the “scripted” development of any health embryo of a species. The word doesn’t mean merelt “change-over-time,” as the Darwinists are always saying it does, but rather, it means “development toward an end-state.”

#John1453: We can directly observe different types of fossils. Evolution is but one potential explanation for the successive differences in types of fossils.

[Z replying] You're confusing the direct observation of evolution, such as in the Grants' observations of evolution in Galápagos Finches, with Common Descent, which is inferred from a variety of evidence from geology to genetics."

The discussion was about fossils, and I meant to say that we do not directly observe evolution when we observe fossils. Z indicates his agreement with this.

As for the implication, one possible, but not only, explanation for the fossils is common descent. As M. astutely pointed out, the fossils are consistent with several explanations and so do not determined our selection of an explanation.

An elaborated nested hierarchy pattern doesn't require artifice: It is the inevitable consequence of the very natural processes of divergence and reproductive isolation.

Artifice is the impact of knowledge and sentience on processes and mechanisms. You've already said that this can be seen in the case of certain organisms. If the impact of the knowledge and intelligence typical to organisms can be seen now then why do you assume that it never had any impact in the past?

Common Descent is one of the most profound facts in biology.

Evolved to:

Common Descent is very well-supported.

Since when are facts "well-supported"?

Sorry, but just saying "common source" is scientifically meaningless.

It's at least as meaningful as imagining things about ancestry and then passing off your own imagination as the equivalent of observable facts. You've already admitted that the impact of knowledge and sentience can be seen in organisms that humans design. If the knowledge typical to organisms can be recognized and detected then why should anyone assume that it never had any impact in the past? A common form of sentience may be the source of much commonality.

Common Descent explains and predicts new observations.

It is based on imagining things about the past and therefore perfectly predicts everything that has been observed. That is why you cannot show that the opposite observation would falsify it.

E.g.For instance, we can often predict the characteristics of intermediate organisms and then find their fossils in the appropriate strata.

You could predict the exact opposite just as easily.

But even given the remarkably "soft" science typical to vague notions of common descent the Coelacanth illustrates that "predicting" or specifying things based on imagining things about skeletal remains is falsifiable in rare instances. The Coelacanth was once imagined to “fit” as Tiktaalik is now based on its skeletal remains. It was considered a “transitional” form based on imaginary soft anatomy yet when discovered alive and observed its soft anatomy did not match what was imagined. And even what was imagined with respect to its skeletal remains was not true given that it did not use its bony fins to “walk,” etc. I will not bother citing some of the imaginative tales told of the Coelacanth walking around and so on but I would note that it is curious that on the rare occasions when mythological narratives typical to vague notions of common descent can be put to the test they have been. The whole process of imagining things in this way seems to have more to do with mythologies of progress than experimental or empirical science and they are often seamlessly woven into broader narratives of progress and so contain the ironies typical to progress:Confident that her fossil showed evolution better than Tiktaalik, Boisvert and other Darwinists then proceeded to admit striking criticisms of Tiktaalik: The interview with Boisvert at The Scientist states, “Previous data from another ancient fish called Tiktaalik showed distal radials as well — although the quality of that specimen was poor. And the orientation of the radials did not seem to match the way modern fingers and toes radiate from a joint, parallel to each other.”The “quality” of Tiktaalik as a fossil specimen was “poor”? When did we see Darwinists admit this previously? Never. They wouldn’t dare make such admissions until they thought they had something better.Moreover, now that we have Panderichthys, Darwinists are openly admitting that the orientation of Tiktaalik’s radials do “not seem to match the way modern fingers and toes radiate from a joint.” The Rise and Fall of Tiktaalik

No, it's what is known as an important point. You're not systematically identifying lines of ancestry based on "uncrossed lines" and mathematical relationships, you're imagining it based on inferences which may or may not be reasonable.

We could dig up a family cemetary and not be able to determine the exact relationships, even if we might be able to determine that they are all cousins of one order or another.

It seems to me that there's not much there to determine given that you've already assumed that everything alive from a fungus to a human are all cousins "of one order or another." Apparently one could dig anywhere and that conclusion would already be determined. You're a bit vague on this point though, given that life may have a few origins and so on, in which case every living thing might not be cousins.

When we find a fossil, we can never be sure they are on the direct line of descent.

That's generally why you have to imagine things about descent. It's actually surprising that it's not easier to imagine things about the past given that a fossil is typically just the skeleton.

These people are so invested, there are such True Believers, that they have trained themselves to not see their circular reasoning ... even when it's explicitly, and repeatedly, pointed out and explained.

As we have directly observed speciation, we have therefore seen new taxa being created.

laugh out loud: And teh modern lungfish is close to the transitional condition, also.

The modern lungfish is derived, but does have intermediate features. As this was discussed in Origin of Species way back in 1859 as evidence to support Darwin's theory, it's odd you would bring it up as if it were a new insight.

laugh out loud: Adn have we actually observed hwo long it takes for one species to turn into another?

Ilíon: 1) Mere speciation is a distraction from “what evolution means,” and the distraction appears to be intentional of the part of the evolutionists.

Reproductive isolation is a component of the Theory of Evolution.

Ilíon: 2) The actual meaning of the word ‘evolution’ is nothing at all like (Darwinistic) evolutionists use it … it’s for this reason that St. Chuckie avoided the word, using instead the awkward locution, “descent with modification,”

mynym: Artifice is the impact of knowledge and sentience on processes and mechanisms. You've already said that this can be seen in the case of certain organisms.

Humans are capable of artifice.

mynym: If the impact of the knowledge and intelligence typical to organisms can be seen now then why do you assume that it never had any impact in the past?

We don't make that assumption. There's just no such evidence, and significant evidence of natural mechanisms. The only assumptions we make are those held tentatively for the purposes of empirical verifications.

Zachriel: Common Descent is one of the most profound facts in biology.

mynym: Evolved to:

Zachriel: Common Descent is very well-supported.

Universal gravitation (as applies to apples and planets) is one of the most profound facts in physics. Universal gravitation is very well-supported.

mynym: If the knowledge typical to organisms can be recognized and detected then why should anyone assume that it never had any impact in the past?

Quite possibly. There's just no such evidence, with ample evidence pointing to natural processes.

Zachriel: Common Descent explains and predicts new observations.

mynym: It is based on imagining things about the past and therefore perfectly predicts everything that has been observed.

Common Descent predicts new observations. That's why scientists spent years in the Canadian Arctic looking for an organism with predicted intermediate traits.

Ilíon: These people are so invested, there are such True Believers, that they have trained themselves to not see their circular reasoning ... even when it's explicitly, and repeatedly, pointed out and explained.

The reason we know it's not circular reasoning is because the Theory of Evolution leads to predictions of novel observations. When someone can make a prediction from theory, walk out into the wastelands of the Sahara, and pull out the fossil skeleton of a whale with hind limbs, we know it's not just guesswork or circular reasoning. The Theory of Evolution has been so fruitful that, since its inception, it has not only led to new discoveries, but entire new scientific fields.

At what point in the past does this no longer apply? I.e. at what point should we begin to seek to reduce organisms to things that seem like blind, ignorant processes to us? Apparently you admit that it does not apply to us now as thinking, knowing and seeing beings capable of artifice so at what point in the past must be begin imagining mythological narratives of naturalism based on nothing but blind and ignorant processes? Similarly, if humans are capable of artifice as organisms at which point do we say that the apparent intelligence of other organisms must be reduced to things that seem like blind and ignorant processes?

We don't make that assumption. There's just no such evidence...

Well, what would such evidence look like?

...and significant evidence of natural mechanisms.

It would seem so, whatever natural means in a reality in which naturalists say that multiple natures/universes may exist. But is it possible to find evidence of unnatural mechanisms? Is there such a thing as evidence of supernatural mechanisms? If not then why are you bothering to say that the evidence supports naturalism? That is merely as it must be given your assumption that all observations are natural, whatever that means.

Quite possibly. There's just no such evidence...

I hope that you're not surprised by that given that there apparently cannot be such evidence. If there can be such evidence in biology then what would it look like? At a wider level, isn't it true that all evidence must be natural in order to be observed in nature?

Humans have always been capable of artifice. It's one of their distinguishing features. Their immediate relatives also have the capability of fashioning tools.

mynym: I.e. at what point should we begin to seek to reduce organisms to things that seem like blind, ignorant processes to us?

That's not a very clear statement. But the evidence supports natural processes, not artifice.

mynym: Well, what would such evidence look like?

It's hard to tell. You would have to propose a specific hypothesis. The Theory of Evolution provides for robust mechanisms that can reasonably account for the observed patterns, but that doesn't mean an alien monolith didn't tamper with the hominid genome at some point in the past.

mynym: But is it possible to find evidence of unnatural mechanisms?

Try to not equivocate on "natural." We're using it in the sense of artifice and non-artifice. There is ample evidence of artificial mechanisms.

The reason we know it's not circular reasoning is because the Theory of Evolution leads to predictions of novel observations.

There is no singular theory of evolution. Evolution is generally just an unfalsifiable gloss that can be added to everything that has been observed or discovered. Biologists are still trying to deal with their creationist past in many ways. They used to add a different gloss to their discoveries, now another. Their criticisms of the old gloss applies usually applies equally to the new, e.g.:One cannot directly study, observe, or experiment with this real-one accepts it on faith. If one assumes the existence and operation of [imaginary] forces, nothing is impossible.

Or, an evolutionist accepted on faith that there is [common descent] and then arranged his observations about living organisms in such a fashion to suggest that life was so [progressive] that it could [just happen].

And so on.

The Theory of Evolution has been so fruitful that, since its inception, it has not only led to new discoveries, but entire new scientific fields.

Many have sought to synthesize it with and add it as a gloss to different fields of study but it's not clear that it has added much to anything, mainly because it generally hasn't been rigorously specified in the first place. (Vague notions of common descent based on nested hierarchies without much knowledge of actual ancestry or mechanisms by which such an ancestry would or could be produced notwithstanding.)

Humans have always been capable of artifice. It's one of their distinguishing features. Their immediate relatives also have the capability of fashioning tools.

You stated earlier that this capacity for artifice can be detected in other organisms that humans design. Can it be detected in humans themselves? Do they have the capability of fashioning their own bodies as a tool or a means toward an end?

The Theory of Evolution provides for robust mechanisms that can reasonably account for the observed patterns...

Ironically the more it provides, the less it specifies.

Try to not equivocate on "natural." We're using it in the sense of artifice and non-artifice. There is ample evidence of artificial mechanisms.

I'm not equivocating on anything. I'm well aware that I do not know what terms like natural and artificial mean in your mind. That's why I ask so many questions. It's still not clear how your apparent dichotomy is specified, that's why I ask if humans are capable of being artificial within their own bodies (Using them as a tool with ends in mind and so on.) and so on.

Zachriel: Having established Common Descent, we can discuss those various theories. But there is no escaping the fact that life has descended from common ancestors.

Sure, but common descent is also true of designed systems. Modern computers are all descended from earlier and more primitive artifacts. Common descent does not prove natural evolution any more than it proves design. I personally think that such evidence is more in keeping with design since we have existence proof of common descent in design.

At any rate, strict common descent in the Darwinian sense does not seem to be what occurred. There are organisms that share features from parallel branches of the tree of life even though they seem to have been separated from those branches before those features appeared. Somehow, 'lateral descent' has a funny ring to it.

Louis, "Modern computers are all descended from earlier and more primitive artifacts"

Please explain how silicon chips are homologous to vacuum tubes, or how the processor in a calculator is homologous to an abacus. you can start by explaining how they use the same parts in the same arrangement.

Ilíon: The correct response is to refuse to answer their motive-mongering. The correct response is to point out the logically flawed reasoning of their motive-mongering (and, if one wishes, to mock it).

You're probably right, but it's fun to watch their mindset in action. Strawman arguments are infuriating but interesting all the same. It shows what they're fighting against.

abimer automatically assumed that I believe in an all-knowing, omnipotent god to make a silly point, but I don't. Such a god would not need to design or create anything. It's a silly concept, in my opinion.

As a Christian, I believe that the creators (the elohim in Genesis) experimented for billions of years before they could take a step back and say to themselves "this is really good".

abimer would be confounded by this stance because this is not what he/she is fighting against. It occurred to me that evolutionists and atheists are reactionaries more than anything else. They are reacting against their own upbringing and they do it without regard to the truth. Their motive is to defeat that mythical beast in their heads.

Louis Savain: There are organisms that share features from parallel branches of the tree of life even though they seem to have been separated from those branches before those features appeared.

There are some crosses. Ironically, these crosses often provide some of the best evidence of Common Descent.

When first examining genomes, most DNA in the human lineage was found to closely resemble other primates. But surprisingly, there were bits-and-pieces that seemed to belong to viruses. Once inserted into the phylogenetic tree, they formed their own nested hierarchy, just as if a viruses had inserted themselves into various points of the ancestry. And it turns out that viruses can and will insert their material into germ cells.

Scientists can and do make, test and verify empirical predictions entailed in the Theory of Evolution. Your comments do not address that point.

But it is also a gloss or creation myth that can be or is added to every single discovery. It may even be that it can be added to all possible discoveries, supposedly all other than centaurs. You've only addressed this point by pointing to it at its most specified but it's important to point out that many are "overwhelmed" with mental illusions rooted in unfalsifiable claims in general. It's one thing to believe in unfalsifiable things which may be reasonable, it's another to say that your beliefs about history and common ancestry are the equivalent of some type of falsifiable, experimental and empirical science. The philosopher David Stove wrote a book criticizing evolutionary science, yet he still believed in common descent. Behe did the same but what seems to get propagandists like Prothero quite upset is not the science but when people are not some type of "true believers." He's one step from specifying some form of confession of faith and establishing a community of believers who must shun anyone who does not share the same beliefs:A good example is Kurt Wise, who is famous as one of the few young earth creationists with a legitimate background in paleontology; he actually got his Ph.D. at Harvard....He entered Havard as a student of Stephen J. Gould but apparently did not reveal his creationism to Gould or Harvard when he was admitted. I am not aware of what Gould thought when he found out that he had a creationist among his students... What's the point of going through the long ordeal of obtaining a Ph.D. if you're never going to learn something new, or be challenged and think hard about your beliefs? More importantly, if you're doing all this work to obtain a degree but don't believe in any of the stuff you said or wrote, isn't that dishonest and fraudulent? Science is a social network based on trust and reputation....how can other scientists trust whether he biased his data collection or analysis or whether he just made it up in order to fit his preconceptions? [How ironic...] We will see elsewhere in this book how this kind of dishonest science is common among other creationists whose backgrounds are irrelevant to the stuff they are promoting, but the question is now relevant even with Harvard-trained scientists like Wise. (Evolution: What the Fossils Say and Why It Matters by Donald Prothero :22-23) (Emphasis added)

It seems like he is saying that one must truly believe themselves to be a distant cousin with a worm in order to do sound science. He may even be saying that a person must believe themselves to be the product of ignorant processes in order for their scientia/knowledge have integrity. That's odd. It's also odd how many people who have not "truly" believed as he does who have caused progress in science and progress in general, while many people who have been true believers (e.g. the whole eugenics movement) have retarded scientific progress based on Darwinian pseudo-science, not to mention helping to destroy whole civilizations.

I'm still interested in this:Zach says:Humans have always been capable of artifice. It's one of their distinguishing features. Their immediate relatives also have the capability of fashioning tools.

You stated earlier that this capacity for artifice can be detected in other organisms that humans design. Can it be detected in humans themselves? Do they have the capability of fashioning their own bodies as a tool or a means toward an end?

Zachriel: Scientists can and do make, test and verify empirical predictions entailed in the Theory of Evolution. Your comments do not address that point.

mynym: But ...

But what? On the one side we have scientists who repeatedly test entailments of the Theory of Evolution, and on the other what?

mynym: But it is also a gloss or creation myth that can be or is added to every single discovery.

So hypothesis-testing vs. handwaving.

mynym: It's one thing to believe in unfalsifiable things which may be reasonable, it's another to say that your beliefs about history and common ancestry are the equivalent of some type of falsifiable, experimental and empirical science.

Each of the primary claims of the Theory of Evolution are falsifiable and well-tested.

mynym: You stated earlier that this capacity for artifice can be detected in other organisms that humans design. Can it be detected in humans themselves? Do they have the capability of fashioning their own bodies as a tool or a means toward an end?

It's difficult to know what you are attempting to say. If it just means volition, then yes, humans have volition.

========Your arguments that the nested hierarchy (tree of life) only fits a Darwinian evolution are unconvincing.========

Such arguments may or may not be convincing, but in any case they are not from empirical science. The "only evolution can explain X" is a statement that assumes full knowledge of the science at hand and of all possible explanations. It is equivalent to an "if an only if" statement, which cannot be argued from a scientific perspective.

========The nested hierarchy of genomes, morphology, embryonics, biogeography, fossils in time, is strong evidence of Common Descent. Common Descent is a profoundly important fact about biology. It means humans descended from ancestral hominids that descended from ancestral primates. There are many biological theories that might conceivably be consistent with Common Descent.

Having established Common Descent, we can discuss those various theories. But there is no escaping the fact that life has descended from common ancestors.========

This is a common example of the unspoken anti realism in evolutionary thought. Empirical evidence is ignored wholesale for the sake of the theory. See for example:

Cornelius Hunter: This is a common example of the unspoken anti realism in evolutionary thought. Empirical evidence is ignored wholesale for the sake of the theory.

Sorry, that is incorrect. It's all about the empirical evidence. The signal for the nested hierarchy is very strong across many taxa, including vertebrates. There is simply no way to deny that there are very strong correlations across large numbers of traits.

My choice of the computer as an example of a designed but hierarchically evolved technology was off the top of my head and may not have been perfect but it still shows a tree-like hierarchy in various places along its evolution.

Let me add that the tree is such a powerful design tool that it is a fundamental aspect of Project COSA, a novel parallel programming project based on design composition and reuse. See COSA: A New Kind of Programming if you're interested in the future of parallel programming.

If I were a genetic engineer in charge of creating new lifeforms, I would use a tree-like structure for storing my designs. In fact, even though my knowledge in this area is minimal, I'd be willing to bet that the genome itself is organized like a tree and uses some sort of tree-like control hierarchy with many control branches.

Louis Savain: My choice of the computer as an example of a designed but hierarchically evolved technology was off the top of my head and may not have been perfect but it still shows a tree-like hierarchy in various places along its evolution.

We can construct all sorts of trees, but in biology, there is only one reasonable, objective tree.

Consider vehicles. The most obvious grouping is by manufacturer, make and model. But that conflicts with grouping by truck, sedan, coupe, motorcycle. And that conflicts with grouping by engine or brakes or radios. Mixing-and-matching is a hallmark of design.

With biology, each lineage has its own "designer" who can't see anything in any other lineage. If an organism needs wings, it might be a modified exoskeleton (insects), skin stretched between "pinkie" to leg (pterosaurs), feathers on arms (birds), skin stretched across fingers (bats). That's because the "designer" of the bat can't borrow feathers from birds. Each lineage, materials and methods, is kept separate. The cases of convergence and crosses often help prove the general principle.

This is not a trivial pattern. It means we can look at a jaw comprised of a single bone with heterodont dentiton and determine that the organism cared for its young. Imagine that! Nothing but an old fossilized jaw of a long-dead organism, and we can determine aspects of its most intimate behavior.

These correlations apply across traits as varied as skeletons and molecules. You can't do the same for brakes or car radios.

Louis Savain: If I were a genetic engineer in charge of creating new lifeforms, I would use a tree-like structure for storing my designs.

If you were a genetic engineer, you would insert a human insulin gene into a bacterium to make human insulin so that people wouldn't have to rely on porcine insulin.

Louis Savain: I'd be willing to bet that the genome itself is organized like a tree and uses some sort of tree-like control hierarchy with many control branches.

Okay so have we observed any new structures organs, or functions form.

Zachriel:

My point about the lungfish was thah the fact that the tiktaalik, something near the transitional condition, was found to live at a certain time in geological history is not significant, because we have lungfish that exist now.

From what I've read, the majority of cases of evolution do not proceed by polyploidy alone. And polyploidy doesn't work very well in species that are not angiosperms. in most case you have tp copy a gene during meitosis, then chaneg the gene incrementally. This takes a long time. According to this article: http://www.genetics.org/cgi/content/full/180/3/1501

for an adaptaion that takes two simple mutations to work its way through a population of oranisms that reproduce at the rate humans do, takes ~100,000,000 years. But evolution happens two quickly to be caught by the fossil record.

laugh out loud: My point about the lungfish was thah the fact that the tiktaalik, something near the transitional condition, was found to live at a certain time in geological history is not significant, because we have lungfish that exist now.

Living fossils were cited by Darwin in Origin of Species. Do you understand why he consider this important evidence? We can look at extant organisms for intermediates, just as we can look at fossil organisms. A lungfish is still fit for its particular habitat, even though it shares a common ancestor with organisms that transitioned to terrestrial life. That doesn't mean that lungfish haven't evolved, just that the trait is similar to the ancestral form.

Tiktaalik has an array of predicted intermediate features expected of an organism close to the transition.

Shubin, Daeschler & Jenkins The pectoral fin of Tiktaalik roseae and the origin of the tetrapod, Nature 2006.

laugh out loud: Adn have we actually observed hwo long it takes for one species to turn into another?

Zachriel: It depends. It happen very quickly, such as with polyploidy

laugh out loud: From what I've read, the majority of cases of evolution do not proceed by polyploidy alone.

It's an example. Once organisms become reproductively isolated, they tend to diverge. Such divergence naturally leads to a nested hierarchy. It doesn't take design to form such a pattern, and it doesn't take magic. Just descent with modification along uncrossed lines.

Another type of speciation is due to chromosome rearrangement, such as in rodents. Or allopatry and drift. Or hybridization. Or perhaps sometimes sympatric speciation due to diversifying selection. We can observe all these processes of reproductive isolation.

laugh out loud: in most case you have tp copy a gene during meitosis, then chaneg the gene incrementally.

Two specific neutral mutations may never fix in a population. But some neutral muations are always being fixed; they fix at the neutral mutation rate. (Ask if this is not clear.) And if sequential mutations are individually selectable, then they can become fixed very rapidly, even in small populations.

Different kinds of mutation cna happen real fast. The problem is how does this lead to a news species. If it can happen so rapidly why don't we see fruit flies turning into houseflies, or e.coli turning into another bacteria, or dogs turning something other than dogs. At most all we've seen is fruit flies changing their diet, or mosquitoes preferrng people over birds. The standard answer is that we don't observe species to species change because it takes to long for scientists to observe. The article sited above would tend to support this.

You're confusing complex adaptation with mutation and speciation. They are all separate processes.

laugh out loud: If it can happen so rapidly why don't we see fruit flies turning into houseflies

Evolution doesn't predict that fruit flies will turn into houseflies. It predicts they descended from a common ancestor. Complex adaptations take long periods of time. And the housefly niche is already occupied by a highly adapted competitor, the housefly.

laugh out loud: The article sited above would tend to support this.

You didn't seem to notice the response about genetic changes. If sequential mutations are individually selectable, then they can become fixed very rapidly, even in small populations.

laugh out loud: The standard answer is that we don't observe species to species change because it takes to long for scientists to observe.

We do observe species to species changes. But we don't see a giraffe turning into a toad. We don't expect to. That divergence from their common ancestor took hundreds of millions of years.

Zachriel: With biology, each lineage has its own "designer" who can't see anything in any other lineage.

The platypus may beg to differ. In fact, the platypus seems to show the deep sense of humor of the original tree of life designers. They seem to be saying: "Let's use a little bit from disparate branches of the tree of life to create a weird creature so as to confound the unbelievers and make them look like fools." It worked. :-D

Louis Savain: I'd be willing to bet that the genome itself is organized like a tree and uses some sort of tree-like control hierarchy with many control branches.

Tree-like structures are *natural*. Think of, oh, trees.

What you call natural, I call designed. My COSA software component tree is designed by a designer: me. The genetic tree of life was also designed. Lately, I have taken to saying that nature is artificial. Your opinion to the contrary is no better than mine.

Sorry, but no. A platypus is a monotreme. Mammals descended from egg-laying reptiles, and monotremes diverged from that line before marsupials and eutherians. The bill is not a hard keratin structure such as in a bird's bill, but is soft, leathery and sensitive. In other words, it adapted structures from its own lineage. It did not borrow eggs and beaks from birds.

Louis Savain: What you call natural, I call designed.

You can call it whatever you want, but a tree-structure can be created with just a few simple rules based on branching descent. As a programmer, you should know about fractal trees.

Sorry, but no. A platypus is a monotreme. Mammals descended from egg-laying reptiles, and monotremes diverged from that line before marsupials and eutherians. The bill is not a hard keratin structure such as in a bird's bill, but is soft, leathery and sensitive. In other words, it adapted structures from its own lineage. It did not borrow eggs and beaks from birds.

So say you, even though going from cold blooded reptile to warm-blooded mammal is a huge leap for which you have no proof. As Cornelius and ID supporters like to say, it's just another just-so narrative that is not supported by rigorous scientific observation (you weren't there to see it happen naturally via selection and random mutation.

It is possible that your classification of the platypus may very well be true even if it's not proof of Darwinian evolution. A gene designer could have followed the same path down the designed evolutionary tree and obtained the same results. This is the conclusion that I draw from it. You draw your own. But neither is scientific because we weren't there to observe the process. I choose my conclusion because it is infinitely more plausible than random mutations.

Louis Savain: What you call natural, I call designed.

You can call it whatever you want, but a tree-structure can be created with just a few simple rules based on branching descent. As a programmer, you should know about fractal trees.

I note with glee your use of the word "created" above. My point, which you do your best to skirt, is that a tree-like hierarchy is not necessarily proof of evolution because it can be used equally as evidence for design. So it bothers me that evolutionists insist on using it as proof. It is not.

This particular fossil, along with mutations in mice, shows the particular developmental genes responsible for the transition. The amazing thing is that we can actually see the transition whereby bones in the reptilian jaw were coopted to form the mammalian middle ear, resulting in an irreducibly complex structure, each incremental step providing a selectable improvement in hearing.

Louis Savain: As Cornelius and ID supporters like to say, it's just another just-so narrative that is not supported by rigorous scientific observation (you weren't there to see it happen naturally via selection and random mutation.

Descent with modification is plainly revealed in the fossil record. You might quibble about mechanisms, but that discussion is not possible when you refuse to acknowledge descent with modification.

Louis Savain: It is possible that your classification of the platypus may very well be true even if it's not proof of Darwinian evolution.

It's the difference between scientists who care enough to actually study the platypus, and those who ignorantly point to it for some other purpose.

Louis Savain: A gene designer could have followed the same path down the designed evolutionary tree and obtained the same results.

We could perhaps engage that discussion, but you can't pretend to be talking about the evidence when you neglect the substantial evidence of descent with modification, including morphological, genetic, embryonic, biogeographical, and fossils in time.

Louis Savain: My point, which you do your best to skirt, is that a tree-like hierarchy is not necessarily proof of evolution because it can be used equally as evidence for design.

In the old days, the complicated dance of the planets across the sky led even the wisest scholars to say that they were designed. Only the most complex human device, the astrolabe, could begin to emulate the complexity of the Celestial Spheres. But then Newton discovered he could explain everything with a few simple rules, the same rules that applied to objects on Earth. Sadly, the angels became superfluous.

If you are really interested, then you have to be willing to examine the evidence. The first correlation you might consider is that if you look at a lower jaw comprised of a single bone with heterodont dentition, then you can predict that the organism cared for its young. The nested hierarchy is a very important pattern in biology that applies across many taxa. Then we need to look at a few fossil transitions, such as reptile to mammal, whereby you can easily see the process of descent with modification including evidence of selectable, incremental changes, such as the evolution of the mammalian middle ear. Then we can look at directly observable mechanisms, such as natural selection and sources of variation.

====We can predict it will have a complex eukaryote cell structure with organelles, ingest other organisms for nourishment, bilateral symmetry, alimentary canal, have a bony head at one end with an array of sense organs, vertebrae protecting a nerve cord, integument, jaw, ribs, four limbs during at least at some stage of life, neck, neocortex, endothermic, internal fertilization, four-chambered heart, lungs with alveoli and a muscular diaphragm, two eyes, three ear bones in each of two ears, hair or at least hair follicles at some stage of life, sebaceous glands, most will have heterodont dentition, etc. ====

So complex adaptation happens real slow, but it happens too fast to get caught by the fossil record. And my example of fruit fly to housefly was just that, an example. Why haven't we seen a signinficant change in fruit flies? Or dogs? The standard answer is that it happens too slowly for humans to see.

The case at issue, mammary glands, leads to a number of specific empirical predictions, from cell structure to the number of bones in the middle ear. We can reverse the order and from a lower jaw comprised of a single bone with heterodont dentition, predict all those other traits, as well as that the organism cared for its young.

All from the jaw bone of an ass.

Remember, this concerned Ilíon's suggestion that the nested hierarchy was due simply to the "well-known human propensity for seeing patterns where there are none." Because we can make very specific empirical predictions, this indicates taht the patterns are not due to observational bias, but represent real patterns in nature.

One of George Cuvier’s students dressed as the Devil with horns on his head and hoof-shaped shoes burst into Cuvier’s bedroom when he was asleep and said, “I am the Devil. I have come to devour you!” Cuvier woke up and replied, “I doubt whether you can. You have horns and hooves. You eat only plants.”

Ilíon: Question: Isn't it the case that any nested hierarchy is also consistent with multiple hypotheses, non-exhaustively including:1) Special creation;2) Progressive creation;3) "Front-loading" evolution;4) "Interventionist" evolution;5) No evolution at all, but rather the well-known human propensity for seeong patterns where there are none.

Answer: Why, yes, it is true that nested hierarchies are logically consistent with multiple hypotheses.

Logical implication: Nested hierarchies are underdetermined with respect to Darwinism, and the Darwinist who attempts to brandish them as evidence for Darwinism is engaging in various logical fallacies, including the perennial favorites: circular reasoning and special-pleading.

In other words, you are claiming that each item on your list constitutes a valid hypothesis. We have addressed 5) No evolution at all, but rather the well-known human propensity for seeong patterns where there are none. It is not a valid hypothesis, and is contradicted by the evidence.

Once you remove that from the list, we can address the rest of your comment. Notice that it has been 3 days, 23 hours and 37 minutes since we posted a correction to the time of your latest comment, and yet it still remains on your list.

Progress is rarely possible when discussing Intelligent Design for just this reason. Even the simplest points are never resolved.

Furthermore, others have directly addressed this question. Some have confused empirical evidence with a logical fallacy; another thought the platypus violates the nested hierarchy; still another thinking that the difficulty of resolving ancient divergences means that the nested hierarchy doesn't apply to those transitions, or that every cross means there is no pattern at all.

But there is an objective pattern. We know because it leads to valid empirical predictions. If you want to discuss Common Descent, then you have to recognize the nested hierarchy. And if you want to discuss the posited mechanisms of evolutionary divergence, then you have to discuss Common Descent.

I am looking for the answer all the way at the botttom on Mount Improable. down to the atoms and the molecules that have been created from the mixture of these particles. How DNA formed and how the molecular machines came to be. There is a huge cliff that can't be climbed, it can't be explained because DNA molecules work like a program containing millions of digits and they work within a opertating machine; a machin with parts that natural selection can't accomplish. But to speculate, there must have somehow come into existence a replicator molecule. thats imagination at work. the DNA strand holds a massive code. DNA is what is said to hold the data that creates the next organism; offspring.

You evolutionists or atheists may think that God did not create the earth, but He did, and it was a miracle. He created us sinless and perfect. Satan came to the earth and tempted them, creating sin in God's perfect beings. Jesus then died for us on the cross as God's son, and took all of the sin from the past, present, and future so that we could live and go to heaven. The only way we can go is by believing that He DID die for us, and that He resurrected three days later. Then we can go to heaven.